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LOC115801420 CRISPRi-validated cis-regulatory element chr1.3986 [ Homo sapiens (human) ]

Gene ID: 115801420, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115801420
Gene description
CRISPRi-validated cis-regulatory element chr1.3986
Gene type
biological region
Feature type(s)
regulatory: transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the THEMIS2 (thymocyte selection associated family member 2) gene on chromosome 1 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Sep 2019]
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Genomic context

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See LOC115801420 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27867113..27867634)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27707834..27708355)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (28193624..28194145)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903885 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28156772-28157557 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28157558-28158342 Neighboring gene protein phosphatase 1 regulatory subunit 8 Neighboring gene small Cajal body-specific RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 531 Neighboring gene thymocyte selection associated family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28206149-28206649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 532 Neighboring gene replication protein A2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28240839-28241343

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_066078.1 

    Range
    101..622
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    27867113..27867634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    27707834..27708355
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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